The growing demand for low-cost and functional snacks in many developing nations called for interest in the use of locally grown crops as substitutes for costly imported wheat flour. The amino acid composition, antioxidant and anti-inflammatory properties of the cookies from whole wheat, sweet potato, rice bran and peanut (56.25:18.75:5:20; 37.50:37.50:5:20; 18.75:56.25:5:20% as WPRG 1, WPRG 2, WPRG 3) composite flour blends, respectively, were obtained in this study. The 100% whole wheat and 100% refined flours served as control 1 and 2, respectively. The level of hydrophobic and aromatic amino acids was significantly (p < 0.05) high in WPRG 2 (~ 30 and ~ 10%), respectively when compared to others. However, the branched chain amino acids and Fischer ratio was significantly (p < 0.05) high in WPRG 1 (11.40% and 1.29), respectively, which could have contributed to their improved bioactivities. Notably, the composite cookie samples WPRG 1, 2 and 3 had higher hydroxyl (73.86 − 84.16%), DPPH (76.52 − 84.60%) radical scavenging as well as ferric reducing antioxidant (0.64–0.87 mmolFe2+/mg) properties than the control samples WWF and CWF, respectively. On the contrary, the metal chelating activities of the cookies WPRG 1–3 were not significantly (p > 0.05) different from control samples WWF and CWF. The improved amino acid profile and enhanced antioxidant properties of the composite cookies might have effectively influenced their anti-inflammatory properties (IC50; < 26 μg/ml) when compared to the control samples (IC50; ~ 40 μg/ml), respectively. Hence, the cookies that comprised of antioxidants and anti-inflammatory potentials needed in human health, were acceptable by the consumers.Graphical